Forensic Science International-Genetics最新文献

{"title":"Internal validation of the Precision ID GlobalFiler NGS STR panel v2 kit with locus-specific analytical threshold, and with special regard to mixtures and low template DNA detection","authors":"Balázs Kocsis ,&nbsp;Norbert Mátrai ,&nbsp;Gusztáv Bárány ,&nbsp;Gyöngyvér Tömöry ,&nbsp;Attila Heinrich ,&nbsp;Balázs Egyed","doi":"10.1016/j.fsigen.2024.103159","DOIUrl":"10.1016/j.fsigen.2024.103159","url":null,"abstract":"<div><div>We performed an internal laboratory validation of the Precision ID GlobalFiler NGS STR panel v2 kit to assist the introduction of the technology into the routine forensic casework practice. The study was designed and evaluated based not only on the key validation standards like sensitivity, stability, reproducibility, repeatability, mixture, and concordance, but we also tested the effect of reduced input DNA, we measured and applied locus-specific analytical threshold values, tested two different PCR cycle conditions, sequence artifacts and stutters were also analysed. During the study we also tested the new method on real casework samples. The sensitivity study confirmed that adding 500 pg template DNA for library preparation can be optimal at base PCR cycle number (that was 24), because the measured average heterozygote balance was not lower than 0.82, and each allele was detected above the analytical threshold. However, contrary to previous communications, increasing the PCR cycle numbers up to 28 has not resulted the significant elevation of the heterozygote imbalance. According to our results, raised PCR cycle condition (i.e. 28) is appropriate at or below 150 pg total input DNA. For most loci, the calculated AT was lower than the manufacturer’s recommended. Applying the newly established ATs with raised PCR cycle conditions the allele detection sensitivity and reliability increased. We observed allele dropouts only at the 15 pg template DNA experiments with 5 % frequency, that is better to previously published studies. This result indicates that this low amount of DNA (i.e. 15 pg) could be a minimum limit of template input for a potentially successful analysis. In the mixture study the minor contributor could be detected up to 1:19 mixture ratio. We detected minor alleles in all measurements and concentrations above the threshold if the template DNA were fixed and only SNP differences were observed between the same alleles of the contributors. To test concordance between the new method and traditional STR genotyping we analysed 58 Hungarian individual samples in parallel. Nearby the detected 248 different length-based alleles on the 31 loci in the sample pool we revealed additional 75 sequence variant alleles, that represent an approximately 23 % increase in the total number of observed alleles. The casework study confirmed that the Precision ID GlobalFiler NGS STR panel v2 kit is effective even in genotyping degraded samples with extremely low levels of DNA, if we apply elevated cycle number for library preparation and use locus-specific analytical thresholds.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103159"},"PeriodicalIF":3.2,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142526046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developmental validation of a multiplex qPCR assay for simultaneous quantification of nuclear and mitochondrial DNA","authors":"Filomena Melchionda ,&nbsp;Mauro Pesaresi ,&nbsp;Federica Alessandrini ,&nbsp;Valerio Onofri ,&nbsp;Chiara Turchi","doi":"10.1016/j.fsigen.2024.103164","DOIUrl":"10.1016/j.fsigen.2024.103164","url":null,"abstract":"<div><div>Quantification of human DNA is key in forensic genetics. A more accurate estimate of the amount of DNA is essential for planning and optimising genotyping assays, as is evaluating the presence of PCR inhibitory substances and DNA degradation status. Multiplex qPCR assays are helpful in forensics because they can quantify different targets simultaneously, thus saving valuable samples, time, and labour. The aim of this study was to highlight the challenges in the developmental validation of a multiplex real-time PCR assay and the drawbacks encountered in translating a previously described and validated assay (SD quants) to a different technology by modifying the dye probes and reagent mix to be used in a different instrument. We developed a TaqMan probe-based multiplex qPCR using reagents and fluorescent probes adapted for the Rotor-Gene 6000 instrument (QIAGEN, Hilden, Germany). The initial assay combined two mitochondrial DNA (mtDNA) and two nuclear DNA (nDNA) targets, with amplification products of different sizes (mtDNA = 69 and 143 bp; nDNA = 71 and 181 bp), to estimate the DNA degradation status and an internal positive control (IPC) to detect potential inhibitors. During the initial testing of the assay, we observed an interaction between the 69 bp mtDNA target and the 71 bp nDNA target probe, and experiments were conducted to resolve this issue without success. We removed the small nDNA target (71 bp) and changed from a 5-plex to a 4-plex qPCR assay (qMIND). The final tetraplex assay was tested on 105 forensic samples and/or small amounts of degraded DNA, such as bones, teeth, fingernails, formalin-fixed paraffin-embedded tissues (FFPE), and hair shaft samples. The quantification results were compared with data acquired from the same samples using another commercially available quantification system commonly used in forensic laboratories. In addition, the short tandem repeat (STR) profiles were investigated to determine their correlation with the quantitative values obtained. Overall, the qPCR assay was robust and reliable for DNA quantification in samples commonly used in forensic practice.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103164"},"PeriodicalIF":3.2,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR-Cas technology in forensic investigations: Principles, applications, and ethical considerations","authors":"Ana Filipa Sobral ,&nbsp;Ricardo Jorge Dinis-Oliveira ,&nbsp;Daniel José Barbosa","doi":"10.1016/j.fsigen.2024.103163","DOIUrl":"10.1016/j.fsigen.2024.103163","url":null,"abstract":"<div><div>CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) systems are adaptive immune systems originally present in bacteria, where they are essential to protect against external genetic elements, including viruses and plasmids. Taking advantage of this system, CRISPR-Cas-based technologies have emerged as incredible tools for precise genome editing, thus significantly advancing several research fields. Forensic sciences represent a multidisciplinary field that explores scientific methods to investigate and resolve legal issues, particularly criminal investigations and subject identification. Consequently, it plays a critical role in the justice system, providing scientific evidence to support judicial investigations. Although less explored, CRISPR-Cas-based methodologies demonstrate strong potential in the field of forensic sciences due to their high accuracy and sensitivity, including DNA profiling and identification, interpretation of crime scene investigations, detection of food contamination or fraud, and other aspects related to environmental forensics. However, using CRISPR-Cas-based methodologies in human samples raises several ethical issues and concerns regarding the potential misuse of individual genetic information. In this manuscript, we provide an overview of potential applications of CRISPR-Cas-based methodologies in several areas of forensic sciences and discuss the legal implications that challenge their routine implementation in this research field.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103163"},"PeriodicalIF":3.2,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring nanopore direct sequencing performance of forensic STRs, SNPs, InDels, and DNA methylation markers in a single assay","authors":"Desiree D.S.H. de Bruin ,&nbsp;Martin A. Haagmans ,&nbsp;Kristiaan J. van der Gaag ,&nbsp;Jerry Hoogenboom ,&nbsp;Natalie E.C. Weiler ,&nbsp;Niccoló Tesi ,&nbsp;Alex Salazar ,&nbsp;Yaran Zhang ,&nbsp;Henne Holstege ,&nbsp;Marcel Reinders ,&nbsp;Amade Aouatef M’charek ,&nbsp;Titia Sijen ,&nbsp;Peter Henneman","doi":"10.1016/j.fsigen.2024.103154","DOIUrl":"10.1016/j.fsigen.2024.103154","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Introduction&lt;/h3&gt;&lt;div&gt;The field of forensic DNA analysis has undergone rapid advancements in recent decades. The integration of massively parallel sequencing (MPS) has notably expanded the forensic toolkit, moving beyond identity matching to predicting phenotypic traits and biogeographical ancestry. This shift is of particular significance in cases where conventional DNA profiling fails to identify a single suspect. Supplementing forensic analyses with estimated biological age may be valuable but involves a complex and time-consuming DNA methylation analysis. This study explores and validates the performance of a comprehensive forensic third-generation sequencing assay utilizing Oxford Nanopore Technologies (ONT) in an adaptive and direct sequencing approach. We incorporated the most widely used forensic markers, i.e., STRs, SNPs, InDels, mitochondrial DNA (mtDNA), and two methylation-based clock classifiers, thereby combining forensic genetic and epigenetic analysis in one single workflow.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods and results&lt;/h3&gt;&lt;div&gt;In our investigation, DNA from six anonymous individuals was sequenced using the ONT standard adaptive direct sequencing approach, reaching a mean percentage of on-target reads ranging from 6.6 % to 7.7 % per sample. ONT data was compared to standard MPS data and Illumina EPIC DNA methylation profiles. Basecalling employed recommended ONT software packages. &lt;em&gt;TREAT&lt;/em&gt; was used for ONT-based analysis of autosomal and Y-chromosome STRs, achieving 90–92 % correct calls depending on allelic read depth thresholds. InDel analyses for two lower-quality samples proved challenging due to inadequate read depth, while the remaining four samples significantly contributed to the observed percentage markers (60.9 %) and correct calls (97.8 %). SNP analysis achieved a 98 % call rate, with only two mismatches and two missed alleles. ONT-generated DNA methylation data demonstrated Pearson’s correlation coefficients with EPIC data ranging from 0.67 to 0.97 for Horvath’s clock. Additional age-associated markers exhibited Pearson’s correlation coefficients with chronological age between 0.14 (ELOVL2) and 0.96 (FHL2) at read depths of &lt;30 and &lt;20, respectively. Despite excluding mtDNA from our targeted sequencing approach, adaptive proof-reading fragments covered the complete mtDNA with an average read depth of 21–72, showing 100 % concordance with reference data.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Discussion&lt;/h3&gt;&lt;div&gt;Our exploratory study using ONT adaptive sequencing for conventional forensic and age associated DNA methylation markers showed high sequencing accuracy for a significant number of markers, showcasing ONT as a promising (epi)genetic forensic method. Future studies must address three critical aspects: determining clear quantity and quality measures and detection thresholds for accuracy, optimizing input DNA quantity for forensic casework expectations, and addressing ethical considerations associated with phenotype a","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103154"},"PeriodicalIF":3.2,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing testing efficacy of high-density SNP microarrays to distinguish pedigrees belonging to the same kinship class","authors":"Shao-Kang Mo ,&nbsp;Qing-Wei Fan ,&nbsp;Xiao-Yan Ma ,&nbsp;Yue-Wen Zhang ,&nbsp;Meng-Wen Jiao ,&nbsp;Ling Wang ,&nbsp;Jiang-Wei Yan","doi":"10.1016/j.fsigen.2024.103162","DOIUrl":"10.1016/j.fsigen.2024.103162","url":null,"abstract":"<div><div>Kinship testing, which involves genotyping genetic markers and comparing their profiles between individuals, holds significant applications in forensic science. However, the prevalent use of independent markers often lacks the discriminatory power to distinguish pedigrees belong to the same kinship class. While numerous studies have attempted to address this challenge through diverse approaches, the testing efficacy of high-density SNP microarrays in combination with the likelihood approach remains unclear.</div><div>In this study, we further explored the utilization of linked autosomal SNPs derived from microarrays with the likelihood approach. Several SNP panels with differing numbers of loci were developed and putative pedigrees were constructed to evaluated to test their efficacy in distinguishing second-degree relationships, including grandparent-grandchild, half-siblings, and avuncular. Our findings indicate that the use of high-density SNP microarrays is theoretically feasible for discriminating second-degree relationships, with balanced classification rates ranging from 0.444 to 0.853.</div><div>Moreover, to optimize the practical effectiveness of discriminating pedigrees belonging to the same kinship class, several other aspects such as adding additional SNPs or an additional relative and examining the effects of genotype errors and population selection were discussed. Our results revealed that the employment of denser marker sets with more accurate genotyping methods may be beneficial. Additionally, the inclusion of additional relatives and the selection of an appropriate reference population also appear to be crucial factors for enhancing the accuracy of kinship testing.</div><div>In conclusion, our study provides insights into the potential of high-density SNPs in kinship testing and highlights the need for further optimization and examination into various factors that may contribute to enhancing testing efficacy.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103162"},"PeriodicalIF":3.2,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142442364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The power of hybridization capture - Illustrated using an expanded gene panel on 100 post mortem samples, focusing on sudden unexplained death","authors":"Daniel Kling ,&nbsp;Emma Adolfsson ,&nbsp;Henrik Gréen ,&nbsp;Anna Gréen","doi":"10.1016/j.fsigen.2024.103160","DOIUrl":"10.1016/j.fsigen.2024.103160","url":null,"abstract":"<div><div>Sudden unexpected death (SUD) is an unexpected event that in many cases are caused by diseases with an underlying genetic background. Forensic molecular autopsy is an approach that has gained wide-spread attention, in part explained by the rapid progress of DNA sequencing techniques. The approach leverages genetic data in combination with medical autopsy findings in post-mortem samples to explore a potential underlying genetic cause of death. Traditional forensic approaches to molecular autopsy focus on a small panel of genes, say &lt;200 genes, with strong association to heart conditions whereas clinical genetics tend to capture entire exomes while subsequently selecting targeted panels bioinformatically. The drop in price and the increased throughput has promoted wider exome sequencing as a viable method to discover genetic variants. We explore a targeted gene panel consisting of 2422 genes, selected based on their broad association to sudden unexplained death. A hybridization capture approach from Twist Bioscience based on double stranded DNA probes was used to target exons of the included genes. We selected and sequenced a total of 98 post-mortem samples from historical forensic autopsy cases where the cause of death could not be unambiguously determined based on medical findings and that had a previous negative molecular autopsy. In the current study, we focus on the performance of the hybridization capture technology on a 2422 gene panel and explore metrics related to sequencing success using a mid-end NextSeq 550 as well as a MiSeq FGx platform. With the latter we demonstrate that our sequence data benefits from 2×300 bp sequencing increasing coverage, in particular, for difficult regions where shadow coverage, i.e. regions outside the probes, are utilized. The results further illustrate a highly uniform capture across the panel of genes (mean fold80=1.5), in turn minimizing excessive sequencing costs to reach sufficient coverage, i.e. 20X. We outline a stepwise procedure to select genes associated with SUD through virtual bioinformatical panels extracting tier of genes with increasing strength of association to SUD. We propose some prioritization strategies to filter variants with highest potential and show that the number of high priority genetic variant requiring manual inspections is few (0–3 for all tiers of genes) when all filters are applied.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103160"},"PeriodicalIF":3.2,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142515270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in forensic genetics: Exploring the potential of long read sequencing","authors":"Marcel Rodrigues Ferreira ,&nbsp;Thássia Mayra Telles Carratto ,&nbsp;Tamara Soledad Frontanilla ,&nbsp;Raphael Severino Bonadio ,&nbsp;Miten Jain ,&nbsp;Silviene Fabiana de Oliveira ,&nbsp;Erick C. Castelli ,&nbsp;Celso Teixeira Mendes-Junior","doi":"10.1016/j.fsigen.2024.103156","DOIUrl":"10.1016/j.fsigen.2024.103156","url":null,"abstract":"<div><div>DNA-based technologies have been used in forensic practice since the mid-1980s. While PCR-based STR genotyping using Capillary Electrophoresis remains the gold standard for generating DNA profiles in routine casework worldwide, the research community is continually seeking alternative methods capable of providing additional information to enhance discrimination power or contribute with new investigative leads. Oxford Nanopore Technologies (ONT) and PacBio third-generation sequencing have revolutionized the field, offering real-time capabilities, single-molecule resolution, and long-read sequencing (LRS). ONT, the pioneer of nanopore sequencing, uses biological nanopores to analyze nucleic acids in real-time. Its devices have revolutionized sequencing and may represent an interesting alternative for forensic research and routine casework, given that it offers unparalleled flexibility in a portable size: it enables sequencing approaches that range widely from PCR-amplified short target regions (e.g., CODIS STRs) to PCR-free whole transcriptome or even ultra-long whole genome sequencing. Despite its higher error rate compared to Illumina sequencing, it can significantly improve accuracy in read alignment against a reference genome or de novo genome assembly. This is achieved by generating long contiguous sequences that correctly assemble repetitive sections and regions with structural variation. Moreover, it allows real-time determination of DNA methylation status from native DNA without the need for bisulfite conversion. LRS enables the analysis of thousands of markers at once, providing phasing information and eliminating the need for multiple assays. This maximizes the information retrieved from a single invaluable sample. In this review, we explore the potential use of LRS in different forensic genetics approaches.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103156"},"PeriodicalIF":3.2,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeography of Y-chromosome haplogroup I-P37.2 in Serbian population groups originating from distinct parts of the Balkan Peninsula","authors":"Milica Mihajlovic Srejic,&nbsp;Vanja Tanasic,&nbsp;Milica Keckarevic Markovic,&nbsp;Miljana Kecmanovic,&nbsp;Dusan Keckarevic","doi":"10.1016/j.fsigen.2024.103152","DOIUrl":"10.1016/j.fsigen.2024.103152","url":null,"abstract":"<div><div>Genetic structure of the contemporary Serbian population was shaped by a long history of turbulent historical and demographical events. The most important migrations of Serbs towards present day Serbia, in the recent history, occurred between the 15th to the 18th century from the regions of Old Herzegovina and Kosovo and Metohija. Previous haplogroup analysis revealed wide spectrum of main haplogroups, among which haplogroup I-P37.2 was the most frequent one in Serbian population groups originating from the Balkan Peninsula. Within this study 464 Serbian males samples from three geographical regions in the Balkan Peninsula inhabited by Serbs: present-day Serbia, regions of Old Herzegovina and Kosovo and Metohija, previously classified as haplogroup I-P37.2, were genotyped using the 22 Y-single nucleotide polymorphisms (Y-SNPs) in order to determine deeper phylogenetic and phylogeographic analysis of haplogroup I-P37.2. Based on SNP typing all samples in the Old Herzegovina and present-day Serbia dataset and 122 out of 128 samples from Kosovo and Metohija were assigned to haplogroup I-L621. Further SNP typing revealed very similar haplogroup distribution in all datasets, with the predominant haplogroup being I-PH908, followed by haplogroup I-Z17855. Analysis within haplogroup I-PH908 distinguished haplogroup I-FT14506 as the most frequent in the Kosovo and Metohija dataset, while haplogroup I-FT16449 was the most frequent in the Old Herzegovina dataset. In the present-day Serbia dataset, occurrence of haplogroups I-FT14506 and I-FT16449 was almost equal, comprising 40.2 % and 34.4 %, respectively. Low level of differentiation, within haplogroup I-PH908, was detected between all datasets, with the lowest one detected between present-day Serbia and Old Herzegovina datasets and highest one between Kosovo and Metohija and Old Herzegovina datasets. Furthermore, median-joining network analysis and shared haplotypes statistics revealed closer genetic relationship between Old Herzegovina and present-day Serbia haplotypes. Results obtained within this study support the thesis that migrations from historical region of Old Herzegovina and geographical region of Kosovo and Metohija, had great contribution on the present-day Serbian population genetic structure. Furthermore, here presented results, gave insight into geographic distribution of detected haplogroups I-Z17855, I-Y4460, I-PH908, I-Y5596, I-Y4882, I-FT14506, I-FT16449 and I-A5913 and analyzed SNPs, enabling further improvement of the geographic resolution of paternal ancestry inference.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103152"},"PeriodicalIF":3.2,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142407392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Demonstration of potential DNA contamination introduced by laboratory consumables using Fluorescein","authors":"Colby M. Hymus,&nbsp;Penny L. Cooper,&nbsp;Marie S. Rye","doi":"10.1016/j.fsigen.2024.103157","DOIUrl":"10.1016/j.fsigen.2024.103157","url":null,"abstract":"<div><div>The development of increasingly efficient DNA extraction and profiling kits has increased the amount of allelic information obtained from trace DNA samples, but also inadvertently, increased the detection of DNA contamination. This study aimed to evaluate the potential of DNA transfer using fluorescein, fluorescent under an alternate light source, in the use of a range of forensically relevant DNA profiling consumables. An evaluation of two pre-lysis methods adopting three different sample tubes, some with deliberate seal damage, showed the PrepFiler™ Automated Forensic DNA Extraction Kit caused leakage and crusting when the rim of the PrepFiler™ LySep column was compromised, but no leakage was observed under the same conditions using the Investigator STAR Lyse&amp;Prep kit. The AutoLys tube showed minimal leakage using the PrepFiler™ chemistry. A DNA extract tube with an external thread, similar to the AutoLys tube, showed no leakage after fridge or freezer storage. However, it highlighted that a centrifugal spin does not guarantee all the DNA will pool at the base of the tube. A comparison of adhesive plate sealing films to 8-well strip caps for sealing 96-well PCR plates showed the adhesive plate sealing films presented a lower risk of DNA transfer, largely due to the adhesion of dispersed liquid on the sticky surface of the film. Overall, this study highlighted a number of variables that may be considered in the development of more refined contamination minimisation protocols in respect to increased sensitivities of DNA profiling.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103157"},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142420098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Human identification of single hair shaft using a mass spectrometry mRNA typing system","authors":"Jiajia Fan ,&nbsp;Huan Yu ,&nbsp;Hailing Yang,&nbsp;Yuxin Zhang,&nbsp;Mingming Zhang,&nbsp;Jiaqi Wang,&nbsp;Zidong Liu,&nbsp;Jinding Liu,&nbsp;Zeqin Li,&nbsp;Gengqian Zhang","doi":"10.1016/j.fsigen.2024.103158","DOIUrl":"10.1016/j.fsigen.2024.103158","url":null,"abstract":"<div><div>Hair is one of the most common forms of forensic biological material at various crime scenes. So far, human identification cannot be effectively accomplished with a single telogen hair encountered in forensic casework due to the detection limit. Emerging studies have revealed RNA as a promising biomarker in hair shafts, while the single telogen hair could not be successfully genotyped even after being examined with the recently developed mRNA typing system. MALDI-TOF MS, the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, enables sensitive and accurate measurement of DNA products. To address this problem and further develop the analysis technology of hairs, we established a mass spectrometry system for human identification based on a single hair shaft using 25 polymorphic SNPs located on 18 mRNA molecules (<em>KRT31, RFK, KRT86, KRT35, PABPC1, KMT2D, LEMD2, TBC1D4, CTC1, PPP1R15A, RBM33, LRRC15, KRT33A, KRTAP12–2, KRT81, AHNAK, KRTAP4–8, FLG2</em>). The forensic application of the detection system was evaluated, and all hair samples used were collected from individuals in Shanxi province. Firstly, we demonstrated that the RNA typing results of a single hair shaft were in perfect concordance with DNA typing results and confirmed the consistency between hairs from different body parts. To assess the potential influence of positions along the hair shaft, 6 cm long hair shafts from the distal end were examined by the MALDI-TOF MS system, whose genotype could be successfully detected. The system was capable of detecting aged samples stored for 390 days and could also be employed on various types of hair samples, such as white hair and permed or dyed hair. Finally, 50 unrelated individuals from Shanxi province were genotyped for the population study, and the CDP of the system in the Shanxi population is 0.998928. In this study, we established a mass spectrometry system for human identification based on a single hair shaft. We used a single hair shaft, rather than multiple hair shafts reported in our previous report, to get a full typing profile. The system sensitivity was substantially enhanced, which provided a valuable strategy for forensic practice to perform human identification using hairs.</div></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":"74 ","pages":"Article 103158"},"PeriodicalIF":3.2,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142434452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}